SARS-CoV-2 testing

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Pucksoppet
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SARS-CoV-2 testing

Post by Pucksoppet » Sat Mar 14, 2020 10:50 pm

I am pretty impressed that antigen-based tests

Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis: (Corresponding author: XueFeng Wang: ORCID iD: 0000-0001-8854-275X)

are apparently already commercially available e.g.:

https://www.biopanda.co.uk/php/products ... ovid19.php
https://www.prodiag.nl/store/corona-vir ... 25-pieces/

As I understand it, PCR is the 'gold standard' as it should be directly measuring viral load, and is capable of giving a positive result before IgM has built up enough to be detectable. The disadvantage being PCR takes time.

I'm wondering if viral-shedding occurs via the digestive tract, and whether one way of determining how things are going might be to take samples at the ingress point of sewage works at a point where the sewage is well-mixed and run PCR on them to give a rough estimate of what is going on in the population as a whole? The absolute numbers won't tell you much, I'd have thought, but changes over time might be a useful thing to measure.
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Re: SARS-CoV-2 testing

Post by basementer » Sat Mar 14, 2020 11:08 pm

Pucksoppet wrote:
Sat Mar 14, 2020 10:50 pm
I'm wondering if viral-shedding occurs via the digestive tract, and whether one way of determining how things are going might be to take samples at the ingress point of sewage works at a point where the sewage is well-mixed and run PCR on them to give a rough estimate of what is going on in the population as a whole? The absolute numbers won't tell you much, I'd have thought, but changes over time might be a useful thing to measure.
The virus is known to be shed in the faeces. One thing that John Campbell has mentioned in his updates is that this puts sewage treatment workers at particular risk.

Whether this could be exploited to get an impression of the trend in infection is an interesting idea.
I'll think of something.

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Sun Mar 15, 2020 5:44 pm

I think testing sewage works for the virus with qPCR would run into an issue in the UK, as sewage is diluted with rainwater runoff so the concentration of the virus would be dependent on recent precipitation. If people start washing their hands more, that would also increase dilution. But you could use it for presence/absence to trace the spread and regress of the infection.
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Re: SARS-CoV-2 testing

Post by KAJ » Sun Mar 15, 2020 6:19 pm

Am I correct ? in my understanding that
  • the RT-PCR test detects the virus, so is only positive for active infections
  • the described antigen test would also be positive for those who had recovered
If so, would the antigen test be more useful than the RT-PCR test for monitoring the progress of the outbreak?

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Re: SARS-CoV-2 testing

Post by shpalman » Sun Mar 15, 2020 6:45 pm

KAJ wrote:
Sun Mar 15, 2020 6:19 pm
Am I correct ? in my understanding that
  • the RT-PCR test detects the virus, so is only positive for active infections
  • the described antigen test would also be positive for those who had recovered
If so, would the antigen test be more useful than the RT-PCR test for monitoring the progress of the outbreak?
I posted a link in the wrong thread in which it was found that the body sheds dead non-infectious virus during the recovery phase.
molto tricky

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Sun Mar 15, 2020 7:01 pm

shpalman wrote:
Sun Mar 15, 2020 6:45 pm
KAJ wrote:
Sun Mar 15, 2020 6:19 pm
Am I correct ? in my understanding that
  • the RT-PCR test detects the virus, so is only positive for active infections
  • the described antigen test would also be positive for those who had recovered
If so, would the antigen test be more useful than the RT-PCR test for monitoring the progress of the outbreak?
I posted a link in the wrong thread in which it was found that the body sheds dead non-infectious virus during the recovery phase.
That post has been moved here: viewtopic.php?p=23072#p23072
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Re: SARS-CoV-2 testing

Post by Pucksoppet » Sun Mar 15, 2020 7:09 pm

Bird on a Fire wrote:
Sun Mar 15, 2020 5:44 pm
I think testing sewage works for the virus with qPCR would run into an issue in the UK, as sewage is diluted with rainwater runoff so the concentration of the virus would be dependent on recent precipitation. If people start washing their hands more, that would also increase dilution. But you could use it for presence/absence to trace the spread and regress of the infection.
Ah well, it was just an idea. I thought it might be a rough-and-ready way of doing whole population sampling. Never mind.

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Sun Mar 15, 2020 7:27 pm

Pucksoppet wrote:
Sun Mar 15, 2020 7:09 pm
Bird on a Fire wrote:
Sun Mar 15, 2020 5:44 pm
I think testing sewage works for the virus with qPCR would run into an issue in the UK, as sewage is diluted with rainwater runoff so the concentration of the virus would be dependent on recent precipitation. If people start washing their hands more, that would also increase dilution. But you could use it for presence/absence to trace the spread and regress of the infection.
Ah well, it was just an idea. I thought it might be a rough-and-ready way of doing whole population sampling. Never mind.
It might work targeted further up the pipeline (so to speak), for instance inlets from apartment blocks or something, before rainwater gets in which I suspect would be the major embuggerance.

Another approach to get around limited PCR capacity would be to combine samples from all individuals in a given sampling unit together, then just qPCR that. Microbiologists often do that when writing with environmental samples.

I've heard of PhD students with PCR experience being asked to volunteer in university testing labs - wonder if things like that will get stepped up? Because ability to test, test, test seems to be key and you're quite right to be thinking about these things!
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Re: SARS-CoV-2 testing

Post by KAJ » Sun Mar 15, 2020 8:01 pm

shpalman wrote:
Sun Mar 15, 2020 6:45 pm
KAJ wrote:
Sun Mar 15, 2020 6:19 pm
Am I correct ? in my understanding that
  • the RT-PCR test detects the virus, so is only positive for active infections
  • the described antigen test would also be positive for those who had recovered
If so, would the antigen test be more useful than the RT-PCR test for monitoring the progress of the outbreak?
I posted a link in the wrong thread in which it was found that the body sheds dead non-infectious virus during the recovery phase.
Thanks. I was thinking of substantially after recovery. I understand (maybe wrongly) that without knowing how many have been infected - whether sickened or not - it is difficult to calculate some outbreak parameters, such as case fatality rate.

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Re: SARS-CoV-2 testing

Post by Pucksoppet » Wed Mar 18, 2020 9:43 am

My understanding is that the PCR test detects the presence of viral RNA. Unfortunately the different types of PCR are given confusingly similar names, so knowing which tests are in use and what they tell you can be difficult to work out, especially for lay-people like me.

See:

https://en.wikipedia.org/wiki/Reverse_t ... n_reaction
https://en.wikipedia.org/wiki/Real-time ... n_reaction

But, PCR detects the presence of RNA, not the presence of viable RNA, so in the later stages of infection when the body is shedding RNA that can't infect other people, it will still be detected.

On the other hand, antibody testing doesn't say if you are currently infected. The body produces two different types of antibody, one named Immunoglobulin M (IgM) in the early stages of the immune response to infection; and one labelled Immunogloblulin G (IgG) in the later stages of infection. Assuming you survive the infection, the levels of IgM decrease to undetectable levels of a period of a few weeks, while the IgG remain in circulation for a period than can be years, providing long term immunity.

So an antibody test for IgM says you have been infected recently (within the past few weeks); and a test for IgG says you have had an infection some time in the past, but you don't know when.

So:
positive PCR - you have viral RNA in your body fluids - you are almost certainly infected now, or recovering from a very recent infection
positive IgM - you are either actively infected, or have recently (within the past few weeks) been infected
positive IgG - you were infected some time in the past. You could still be actively fighting an infection.

The PCR test relies on having reliable markers to identify the viral RNA.
The IgM and IgG tests need reliable specific antigens, as antibodies can bind to a range of targets and a test that is insufficiently specific will claim that you have been exposed to SARS-CoV-2 when in fact you haven't, which would be dangerously misleading.

I am not an expert in immunology or other related fields, so there may well be mistakes in the above. Corrections are welcome.

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Re: SARS-CoV-2 testing

Post by KAJ » Wed Mar 18, 2020 6:55 pm

@Pucksoppet
Thanks, very clear. Caveat noted.

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Re: SARS-CoV-2 testing

Post by sTeamTraen » Wed Mar 18, 2020 7:23 pm

Can someone with relevant knowledge put ballpark figures on what a SARS-CoV-2 test costs, in terms of monetary or other resources?

e.g.:
- litmus-type tongue swab, 5 seconds (I know it's not that)
- pee-on pregnancy test, 60 seconds (I know it's not that either)
- saliva sample, send to lab, 5 minutes of lab technician time
- blood draw, send to lab, 60 minutes of time on a machine that we don't have many of
...
...
- international conference that still can't agree if Barry is positive or not
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Re: SARS-CoV-2 testing

Post by Pucksoppet » Wed Mar 18, 2020 8:38 pm

basementer wrote:
Sat Mar 14, 2020 11:08 pm
Pucksoppet wrote:
Sat Mar 14, 2020 10:50 pm
I'm wondering if viral-shedding occurs via the digestive tract, and whether one way of determining how things are going might be to take samples at the ingress point of sewage works at a point where the sewage is well-mixed and run PCR on them to give a rough estimate of what is going on in the population as a whole? The absolute numbers won't tell you much, I'd have thought, but changes over time might be a useful thing to measure.
The virus is known to be shed in the faeces. One thing that John Campbell has mentioned in his updates is that this puts sewage treatment workers at particular risk.

Whether this could be exploited to get an impression of the trend in infection is an interesting idea.
Someone else, in Norway/Sweden, has had the same idea.

NRK (2020-03-18): Håper kloakken kan gi viktige korona-svar {Hope sewers can give important corona-answers}

Google translate allows one to get the gist.

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Re: SARS-CoV-2 testing

Post by basementer » Wed Mar 18, 2020 9:40 pm

Pucksoppet wrote:
Wed Mar 18, 2020 8:38 pm
basementer wrote:
Sat Mar 14, 2020 11:08 pm
The virus is known to be shed in the faeces. One thing that John Campbell has mentioned in his updates is that this puts sewage treatment workers at particular risk.

Whether this could be exploited to get an impression of the trend in infection is an interesting idea.
Someone else, in Norway/Sweden, has had the same idea.

NRK (2020-03-18): Håper kloakken kan gi viktige korona-svar {Hope sewers can give important corona-answers}

Google translate allows one to get the gist.
I'm pleased to see that sewers are "kloakken", a word that the Romans would have recognised. cloaca maxima
I'll think of something.

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Re: SARS-CoV-2 testing

Post by KAJ » Wed Mar 18, 2020 9:54 pm

sTeamTraen wrote:
Wed Mar 18, 2020 7:23 pm
Can someone with relevant knowledge put ballpark figures on what a SARS-CoV-2 test costs, in terms of monetary or other resources?

e.g.:
- litmus-type tongue swab, 5 seconds (I know it's not that)
- pee-on pregnancy test, 60 seconds (I know it's not that either)
- saliva sample, send to lab, 5 minutes of lab technician time
- blood draw, send to lab, 60 minutes of time on a machine that we don't have many of
...
...
- international conference that still can't agree if Barry is positive or not
Grauniad
One chain of private clinics in the Midlands has ramped up the cost of its home delivery coronavirus testing kit from £149 to £249 in just a matter of days

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Re: SARS-CoV-2 testing

Post by EACLucifer » Wed Mar 18, 2020 10:00 pm

KAJ wrote:
Wed Mar 18, 2020 9:54 pm
sTeamTraen wrote:
Wed Mar 18, 2020 7:23 pm
Can someone with relevant knowledge put ballpark figures on what a SARS-CoV-2 test costs, in terms of monetary or other resources?

e.g.:
- litmus-type tongue swab, 5 seconds (I know it's not that)
- pee-on pregnancy test, 60 seconds (I know it's not that either)
- saliva sample, send to lab, 5 minutes of lab technician time
- blood draw, send to lab, 60 minutes of time on a machine that we don't have many of
...
...
- international conference that still can't agree if Barry is positive or not
Grauniad
One chain of private clinics in the Midlands has ramped up the cost of its home delivery coronavirus testing kit from £149 to £249 in just a matter of days
Somewhat explains why asymptomatic celebs are getting tested and frontline medical personel aren't. That production needs to be used for the greatest good - sorting out the financial side can be postponed.

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Re: SARS-CoV-2 testing

Post by shpalman » Wed Mar 18, 2020 10:54 pm

sTeamTraen wrote:
Wed Mar 18, 2020 7:23 pm
Can someone with relevant knowledge put ballpark figures on what a SARS-CoV-2 test costs, in terms of monetary or other resources?

e.g.:
- litmus-type tongue swab, 5 seconds (I know it's not that)
- pee-on pregnancy test, 60 seconds (I know it's not that either)
- saliva sample, send to lab, 5 minutes of lab technician time
- blood draw, send to lab, 60 minutes of time on a machine that we don't have many of
...
...
- international conference that still can't agree if Barry is positive or not
https://www.theguardian.com/world/2020/ ... d-covid-19 says each swab costs about €15.
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Re: SARS-CoV-2 testing

Post by sTeamTraen » Thu Mar 19, 2020 11:40 am

shpalman wrote:
Wed Mar 18, 2020 10:54 pm
https://www.theguardian.com/world/2020/ ... d-covid-19 says each swab costs about €15.
It says "each swab costs about 15 euros". Does the use of "swab" here refer specifically to the price of the testing materials that are deployed in the field to get a sample (i.e., excluding the cost of processing it), or is this just the standard journalist's way of making their prose more "interesting" by using synonyms even if it causes ambiguity?
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Re: SARS-CoV-2 testing

Post by shpalman » Thu Mar 19, 2020 11:45 am

sTeamTraen wrote:
Thu Mar 19, 2020 11:40 am
shpalman wrote:
Wed Mar 18, 2020 10:54 pm
https://www.theguardian.com/world/2020/ ... d-covid-19 says each swab costs about €15.
It says "each swab costs about 15 euros". Does the use of "swab" here refer specifically to the price of the testing materials that are deployed in the field to get a sample (i.e., excluding the cost of processing it), or is this just the standard journalist's way of making their prose more "interesting" by using synonyms even if it causes ambiguity?
I had the same doubt, which is why I was careful just to quote what the article said.
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Re: SARS-CoV-2 testing

Post by AMS » Thu Mar 19, 2020 12:20 pm

Pucksoppet wrote:
Wed Mar 18, 2020 9:43 am
My understanding is that the PCR test detects the presence of viral RNA. Unfortunately the different types of PCR are given confusingly similar names, so knowing which tests are in use and what they tell you can be difficult to work out, especially for lay-people like me.

See:

https://en.wikipedia.org/wiki/Reverse_t ... n_reaction
https://en.wikipedia.org/wiki/Real-time ... n_reaction

But, PCR detects the presence of RNA, not the presence of viable RNA, so in the later stages of infection when the body is shedding RNA that can't infect other people, it will still be detected.

On the other hand, antibody testing doesn't say if you are currently infected. The body produces two different types of antibody, one named Immunoglobulin M (IgM) in the early stages of the immune response to infection; and one labelled Immunogloblulin G (IgG) in the later stages of infection. Assuming you survive the infection, the levels of IgM decrease to undetectable levels of a period of a few weeks, while the IgG remain in circulation for a period than can be years, providing long term immunity.

So an antibody test for IgM says you have been infected recently (within the past few weeks); and a test for IgG says you have had an infection some time in the past, but you don't know when.

So:
positive PCR - you have viral RNA in your body fluids - you are almost certainly infected now, or recovering from a very recent infection
positive IgM - you are either actively infected, or have recently (within the past few weeks) been infected
positive IgG - you were infected some time in the past. You could still be actively fighting an infection.

The PCR test relies on having reliable markers to identify the viral RNA.
The IgM and IgG tests need reliable specific antigens, as antibodies can bind to a range of targets and a test that is insufficiently specific will claim that you have been exposed to SARS-CoV-2 when in fact you haven't, which would be dangerously misleading.

I am not an expert in immunology or other related fields, so there may well be mistakes in the above. Corrections are welcome.
That's pretty much right. The point where you start making IgG instead of IgM is called class-switching, and is triggered by the cells recognising that they are making a useful antibody. Antibodies are made by specialist cells called B-cells, and each cell makes a single unique antibody sequence (which is a fascinating process in its own right - it involves the cells editing their own genomes).

When a B cell works out that it is making the "right" antibody, it also increases its rate of cell division so that more and more of the antibody can be churned out. Some of these additional cells get "banked" as "memory cells", able to be turned on again quickly when you see the same infection again - these are what give you the long-lasting immunity.

There's also a parallel process going on involving T-cells, which learn to recognize infected cells and kill them, but this is harder to measure in a simple blood sample.

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Re: SARS-CoV-2 testing

Post by shpalman » Thu Mar 19, 2020 1:17 pm

Thanks, this is all very interesting.
AMS wrote:
Thu Mar 19, 2020 12:20 pm
... Some of these additional cells get "banked" as "memory cells", able to be turned on again quickly when you see the same infection again - these are what give you the long-lasting immunity.
Is the projected lack of long-term immunity to COVID-19 due to its mutation rate rather than the memory cells "forgetting"?
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Re: SARS-CoV-2 testing

Post by AMS » Thu Mar 19, 2020 3:56 pm

shpalman wrote:
Thu Mar 19, 2020 1:17 pm
Thanks, this is all very interesting.
AMS wrote:
Thu Mar 19, 2020 12:20 pm
... Some of these additional cells get "banked" as "memory cells", able to be turned on again quickly when you see the same infection again - these are what give you the long-lasting immunity.
Is the projected lack of long-term immunity to COVID-19 due to its mutation rate rather than the memory cells "forgetting"?
I think we're still in the phase of speculating in the absence of hard data, to be honest. Everything is based on extrapolating from other coronaviruses, and since we don't immunise against them, there are big gaps in the data we're extrapolating from too!

Even the case(s) where someone/people retested positive have generated more heat than light (eg were they positive after an earlier false negative? Is it just one case?) A systematic study in Wuhan survivors would be useful as they are furthest along this timeline, and I bet this data is being collected already.

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Re: SARS-CoV-2 testing

Post by Pucksoppet » Thu Mar 19, 2020 8:42 pm

AMS wrote:
Thu Mar 19, 2020 12:20 pm
Pucksoppet wrote:
Wed Mar 18, 2020 9:43 am
My understanding is that the PCR test detects the presence of viral RNA. Unfortunately the different types of PCR are given confusingly similar names, so knowing which tests are in use and what they tell you can be difficult to work out, especially for lay-people like me.

See:

https://en.wikipedia.org/wiki/Reverse_t ... n_reaction
https://en.wikipedia.org/wiki/Real-time ... n_reaction

But, PCR detects the presence of RNA, not the presence of viable RNA, so in the later stages of infection when the body is shedding RNA that can't infect other people, it will still be detected.

On the other hand, antibody testing doesn't say if you are currently infected. The body produces two different types of antibody, one named Immunoglobulin M (IgM) in the early stages of the immune response to infection; and one labelled Immunogloblulin G (IgG) in the later stages of infection. Assuming you survive the infection, the levels of IgM decrease to undetectable levels of a period of a few weeks, while the IgG remain in circulation for a period than can be years, providing long term immunity.

So an antibody test for IgM says you have been infected recently (within the past few weeks); and a test for IgG says you have had an infection some time in the past, but you don't know when.

So:
positive PCR - you have viral RNA in your body fluids - you are almost certainly infected now, or recovering from a very recent infection
positive IgM - you are either actively infected, or have recently (within the past few weeks) been infected
positive IgG - you were infected some time in the past. You could still be actively fighting an infection.

The PCR test relies on having reliable markers to identify the viral RNA.
The IgM and IgG tests need reliable specific antigens, as antibodies can bind to a range of targets and a test that is insufficiently specific will claim that you have been exposed to SARS-CoV-2 when in fact you haven't, which would be dangerously misleading.

I am not an expert in immunology or other related fields, so there may well be mistakes in the above. Corrections are welcome.
That's pretty much right. The point where you start making IgG instead of IgM is called class-switching, and is triggered by the cells recognising that they are making a useful antibody. Antibodies are made by specialist cells called B-cells, and each cell makes a single unique antibody sequence (which is a fascinating process in its own right - it involves the cells editing their own genomes).

When a B cell works out that it is making the "right" antibody, it also increases its rate of cell division so that more and more of the antibody can be churned out. Some of these additional cells get "banked" as "memory cells", able to be turned on again quickly when you see the same infection again - these are what give you the long-lasting immunity.

There's also a parallel process going on involving T-cells, which learn to recognize infected cells and kill them, but this is harder to measure in a simple blood sample.
Thank you for the feedback, and your clarification.

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Re: SARS-CoV-2 testing

Post by EACLucifer » Fri Mar 20, 2020 8:43 am

A lot of people I respect are treating this like a big deal, and it looks to be one to me. However, I don't know enough about this field to know for definite. Thoughts?

A serological assay to detect SARS-CoV-2 seroconversion in humans

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Re: SARS-CoV-2 testing

Post by AMS » Fri Mar 20, 2020 8:57 am

EACLucifer wrote:
Fri Mar 20, 2020 8:43 am
A lot of people I respect are treating this like a big deal, and it looks to be one to me. However, I don't know enough about this field to know for definite. Thoughts?

A serological assay to detect SARS-CoV-2 seroconversion in humans
The funding statement suggests it's likely to be genuine:
Funding Statement
Mount Sinai Health System Translational Science Hub (NIH grant U54TR001433) for supporting sample collection. The work of the Personalized Virology Initiative is supported by institutional funds and philanthropic donations. This work was partially supported by the NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) contract HHSN272201400008C, the Australian National Health and Medical Research Council (NHMRC) NHMRC Program Grant (1071916) and NHMRC Research Fellowship Level B (#1102792), the Academy of Finland and Helsinki University Hospital Funds (TYH2018322). Finally, we want to thank the three COVID19 patients for their contribution to research and wish them a speedy recovery.

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